稻属单拷贝核基因TPI序列分析及其在疣粒野生稻鉴定中的应用

生物技术通报 ›› 2012, Vol. 0 ›› Issue (12): 76-81.

稻属单拷贝核基因TPI序列分析及其在疣粒野生稻鉴定中的应用

宋云¹, 陈岩¹, 徐晗¹, 李明福¹, 刘仕琴²

1 中国检验检疫科学研究院植物检疫研究所，北京 100029 ；2 中国科学院昆明植物研究所，昆明 650204

收稿日期:2012-05-01 修回日期:2013-01-25 出版日期:2012-12-26 发布日期:2013-02-06
基金资助:
: 国家质检总局科技计划项目（2012IK295）, 国家科技支撑计划项目（2012BAK11B01）, 中国检验检疫科学研究院基本科研业务费专项（2012JK004）

Analysis of Single-copy Nuclear TPI Gene Sequences of Oryza L. and ItsApplication in Identification of Oryza granulata

Song Yun¹, Chen Yan¹, Xu Han¹, Li Mingfu¹, Liu Shiqin²

1Institute of Plant Quarantine，Chinese Academy of Inspection and Quarantine，Beijing 100029 ；2Kunming Institute of Botany，ChineseAcademy of Sciences，Kunming 650204

Received:2012-05-01 Revised:2013-01-25 Published:2012-12-26 Online:2013-02-06

摘要/Abstract

摘要： 通过对稻属（Oryza L.）及其近缘属等18 个禾本科植物单拷贝核基因TPI 序列进行扩增和测序，分析其系统进化关系及序列差异，并设计鉴定疣粒野生稻（O. granulata）特异的分子标记。序列分析表明，栽培稻间TPI 基因序列碱基变异少，野生稻相对变异丰富，其中疣粒野生稻变异尤为明显，根据疣粒野生稻的TPI 基因序列特异位点设计引物，利用这一分子标记对疣粒野生稻进行准确鉴定。

关键词: TPI, 基因, 疣粒野生稻, 分子标记, 物种鉴定

Abstract: In this paper, single-copy nuclear TPI genes of Oryza L. and its related genera were amplified and sequenced, we analyzedtheir phylogenetic relationships and sequence differences, designed specific primers for Oryza granulata. Sequences analysis indicate thatthere were few variations between cultivar rice, but many variations between wild rice species, especially sharp variations were found for Oryzagranulata. On the basis of these variations, we designed Oryza granulata specified primers for species identification.

宋云, 陈岩, 徐晗, 李明福, 刘仕琴. 稻属单拷贝核基因TPI序列分析及其在疣粒野生稻鉴定中的应用[J]. 生物技术通报, 2012, 0(12): 76-81.

Song Yun, Chen Yan, Xu Han, Li Mingfu, Liu Shiqin. Analysis of Single-copy Nuclear TPI Gene Sequences of Oryza L. and ItsApplication in Identification of Oryza granulata[J]. Biotechnology Bulletin, 2012, 0(12): 76-81.

参考文献

[1] 范树国, 张再君, 刘林. 中国野生稻遗传资源的保护及其在育种中的利用. 生物多样性, 2000(2)：198-207.
[2] 陈娟, 赵云芬. 野生稻种质资源多样性保护现状及其完善对策
[C] . 中国环境科学学会2009 年学术年会论文集(第3 卷),2009: 687-691.
[3] 钱韦, 谢中稳, 葛颂, 等. 中国疣粒野生稻的分布、濒危现状和保护前景. 植物学报, 2001, 43(12)：1279-1287.
[4] 傅立国. 中国植物红皮书(第一册)[M] . 北京：科学出版社,1992: 314-316.
[5] Bao Y, Lu BR, Ge S. Identification of genomic constitutions of Oryzaspecies with the B and C genomes by the PCR-RFLP method. GeneticResources and Crop Evolution, 2005, 52(1)：69-76.
[6] Chen X, Cho Y, McCouch S. Sequence divergence of rice microsatellitesin Oryza and other plant species. Molecular Genetics and Genomics,2002, 268(3)：331-343.
[7] Temnykh S, DeClerck G, Lukashova A, et al. Computational and experimentalanalysis of microsatellites in rice(Oryza sativa L.)：frequency,length variation, transposon associations, and genetic markerpotential. Genome Research, 2001, 11(8)：1441-1452.
[8] Bao Y, Ge S. Origin and phylogeny of Oryza species with the CDgenome based on multiple-gene sequence data. Plant Systematicsand Evolution, 2004, 249(1)：55-66.
[9] Garris AJ, Tai TH, Coburn J, et al. Genetic structure and diversity inOryza sativa L. Genetics, 2005, 169(3)：1631-1638.
[10] 孙传清, 毛龙, 王振山, 等. 栽培稻和普通野生稻基因组的随机扩增多态性DNA(RAPD)初步分析. 中国水稻科学, 1995,9(1)：1-6.
[11] Morden C, Golden S. psbA genes indicate common ancestry of prochlorophytesand chloroplasts. Nature, 1989, 337(6205)：382-385.
[12] Olmstead RG, Palmer JD. Chloroplast DNA systematics: a reviewof methods and data analysis. American Journal of Botany, 1994, 81(9)：1205-1224.
[13] álvarez I, Wendel JF. Ribosomal ITS sequences and plantphylogenetic inference. Molecular Phylogenetics and Evolution,2003, 29(3)：417-434.
[14] Newton KJ. Plant mitochondrial genomes: organization, expressionand variation. Annual Review of Plant Physiology and PlantMolecular Biology, 1988, 39(1)：503-532.
[15] Adams KL, Palmer JD. Evolution of mitochondrial gene content:gene loss and transfer to the nucleus. Molecular Phylogenetics andEvolution, 2003, 29(3)：380-395.
[16] 郭亚龙, 葛颂. 线粒体nad1 基因内含子在稻族系统学研究中的价值——兼论Porteresia 的系统位置. 植物分类学报, 2004,42(4)：333-344.
[17] Li M, Wunder J, Bissoli G, et al. Development of COS genes as universallyamplifiable markers for phylogenetic reconstructions of closelyrelated plant species. Cladistics, 2008, 24(5)：727-745.
[18] álvarez I, Costa A, Feliner GN. Selecting single-copy nuclear genesfor plant phylogenetics: a preliminary analysis for the Senecioneae(Asteraceae). Journal of Molecular Evolution, 2008, 66(3)：276-291.
[19] Duarte JM, Wall PK, Edger PP, et al. Identification of shared singlecopy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and theirphylogenetic utility across various taxonomic levels. BMC EvolutionaryBiology, 2010, 10(1)：61-79.
[20] 鲍露. 新型COS 标记技术及其在梨属植物系统关系研究中的应用前景. 中国农学通报, 2010, 26(22)：34-39.
[21] Sang T. Utility of low-copy nuclear gene sequences in plantphylogenetics. Crit Rev Biochem Mol Biol, 2002, 37(3)：121-147.
[22] 凡星, 廖莎, 沙莉娜, 等. 猬草及其近缘属植物单拷贝核Pgk1基因序列的系统发育分析. 遗传, 2009, 31(10)：1049-1058.
[23] 徐剑, 周君, 刘晓红, 等. 蜜蜂丙糖磷酸异构酶基因及其编码蛋白的生物信息学分析及分子进化研究. 江苏农业学报,2009, 25(2)：270-275.
[24] Xu Y, Hall TC. Cytosolic triosephosphate isomerase is a single genein rice. Plant Physiology, 1993, 101(2)：683-687.
[25] Zou XH, Zhang FM, Zhang JG, et al. Analysis of 142 genes resolvesthe rapid diversification of the rice genus. Genome Biol, 2008, 9(3)：R49.
[26] 郭亚龙, 葛颂. 稻族的系统发育及其研究进展. 植物分类学报,2006(2)：211-230.
[27] Vaughan DA. The wild relative of rice: a genetic resources handbook[M] . Manila: International rice research institute, 1994:130.
[28] Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionarygenetics analysis using maximum likelihood, evolutionarydistance, and maximum parsimony methods. Mol Biol Evol, 2011,28(10)：2731-2739.
[29] Saitou N, Nei M. The neighbor-joining method: a new method forreconstructing phylogenetic trees. Mol Biol Evol, 1987, 4(4)：406-425.
[30] Kimura M. A simple method for estimating evolutionary rates of basesubstitutions through comparative studies of nucleotide sequences.J Mol Evol, 1980, 16(2)：111-120.
[31] 白松, 蒋小龙, 杨碧. 对加强口岸查验防止植物物种资源流失的思考. 西南农业大学学报：社会科学版, 2009, 7(5)：192-195.
[32] 顾列铭. 中国物种资源：正在消失的宝库. 观察与思考, 2008(7)：46-47.
[33] 李健. “生命海盗”窃取中国物种资源. 中国禽业导刊, 2005,22(7)：8.
[34] 姜广源. 加强野生动植物保护与濒危物种管理. 野生动物,2004(6)：54.
[35] Linder CR, Rieseberg LH. Reconstructing patterns of reticulateevolution in plants. American Journal of Botany, 2004, 91(10)：1700-1708.